add cmake config

.gitignore

@@ -24,7 +24,8 @@ whislerwaveres/
 whislerwavelin/
 whislerwaveHLL/
 hallharrisres/
+subprojects
 
 debug/
 frames/
-pyMHD/pyMHD.cpython*
+pyMHD/pyMHD.cpython*

CMakeLists.txt

@@ -0,0 +1,59 @@
+cmake_minimum_required (VERSION 3.20.1) # released April 8, 2021 - https://www.kitware.com/cmake-3-20-1-available-for-download/
+
+project(PHAREMHD VERSION 0.1 LANGUAGES CXX C)
+
+# Release mode default
+if(NOT CMAKE_BUILD_TYPE)
+  set(CMAKE_BUILD_TYPE "Release" CACHE STRING "" FORCE)
+endif()
+
+
+SET(PYBIND_MIN_VERSION "2.5.0")
+find_package(Python 3.8 COMPONENTS Interpreter Development.Module REQUIRED)
+find_program(Git git)
+include(pybind.cmake)
+
+set(PHAREMHD_PROJECT_DIR ${CMAKE_CURRENT_SOURCE_DIR})
+set(CMAKE_EXPORT_COMPILE_COMMANDS 1)
+
+
+set(CMAKE_CXX_STANDARD 17)
+set(CMAKE_CXX_STANDARD_REQUIRED ON)
+
+include_directories(${CMAKE_CURRENT_SOURCE_DIR}/src)
+
+set(SOURCES
+    src/ConservativeVariables.cpp 
+    src/ConstrainedTransport.cpp
+    src/EquationOfState.cpp
+    src/GodunovFlux.cpp
+    src/Interface.cpp
+    src/ModularityUtils.cpp
+    src/PhareMHD.cpp
+    src/PhysicalConstants.cpp
+    src/PrimitiveVariables.cpp
+    src/RiemannSolver.cpp
+    src/TimeIntegrator.cpp)
+
+set(INCLUDES 
+    src/ConservativeVariables.hpp
+    src/ConstrainedTransport.hpp
+    src/EquationOfState.hpp
+    src/GodunovFlux.hpp
+    src/Interface.hpp
+    src/ModularityUtils.hpp
+    src/PhareMHD.hpp
+    src/PhysicalConstants.hpp
+    src/PrimitiveVariables.hpp
+    src/RiemannSolver.hpp
+    src/TimeIntegrator.hpp)
+
+add_library(phareMHD SHARED ${SOURCES} ${INCLUDES})
+
+
+pybind11_add_module(pyMHD pyMHD/pyMHD.cpp)
+target_link_libraries(pyMHD PUBLIC phareMHD)
+
+
+
+

diagnostics/alfvenwave2D/alfvenwave2D.py

@@ -1,5 +1,6 @@
 import sys
-sys.path.append('/home/caromel/Documents/PHAREMHD/pyMHD')
+
+# sys.path.append('/home/caromel/Documents/PHAREMHD/pyMHD')
 
 import numpy as np
 import pyMHD as p
@@ -27,47 +28,56 @@
 dumpvariables = p.dumpVariables.Conservative
 
 ##############################################################################################################################################################################
-lx=nx*Dx
-ly=ny*Dy
+lx = nx * Dx
+ly = ny * Dy
 
 alpha = np.arctan(0.5)
 cosalpha = np.cos(alpha)
 sinalpha = np.sin(alpha)
-kx = 2*np.pi/(cosalpha*lx)
-ky = 2*np.pi/(sinalpha*ly)
+kx = 2 * np.pi / (cosalpha * lx)
+ky = 2 * np.pi / (sinalpha * ly)
+
 
 def rho_(x, y):
     return 1.0
 
+
 def vx_(x, y):
-    return (-1e-4 * np.sin(kx * x * cosalpha + ky * y * sinalpha)) / (2. * sinalpha)
+    return (-1e-4 * np.sin(kx * x * cosalpha + ky * y * sinalpha)) / (2.0 * sinalpha)
+
 
 def vy_(x, y):
-    return (1e-4 * np.sin(kx * x * cosalpha + ky * y * sinalpha)) / (2. * cosalpha)
+    return (1e-4 * np.sin(kx * x * cosalpha + ky * y * sinalpha)) / (2.0 * cosalpha)
+
 
 def vz_(x, y):
     return 0.0
 
+
 def Bx_(x, y):
-    return (1 - 1e-4 * np.sin(kx * x * cosalpha + ky * y * sinalpha)) / (2. * sinalpha)
+    return (1 - 1e-4 * np.sin(kx * x * cosalpha + ky * y * sinalpha)) / (2.0 * sinalpha)
+
 
 def By_(x, y):
-    return (1 + 1e-4 * np.sin(kx * x * cosalpha + ky * y * sinalpha)) / (2. * cosalpha)
+    return (1 + 1e-4 * np.sin(kx * x * cosalpha + ky * y * sinalpha)) / (2.0 * cosalpha)
+
 
 def Bz_(x, y):
     return 0.0
 
+
 def P_(x, y):
     return 0.1
 
+
 x = np.arange(nx) * Dx + 0.5 * Dx
 y = np.arange(ny) * Dy + 0.5 * Dy
-xf = np.arange(nx+1) * Dx
-yf = np.arange(ny+1) * Dy
+xf = np.arange(nx + 1) * Dx
+yf = np.arange(ny + 1) * Dy
 
-xx, yy = np.meshgrid(x, y, indexing = 'ij')
-xfx, yfx = np.meshgrid(xf, y, indexing = 'ij')
-xfy, yfy = np.meshgrid(x, yf, indexing = 'ij')
+xx, yy = np.meshgrid(x, y, indexing="ij")
+xfx, yfx = np.meshgrid(xf, y, indexing="ij")
+xfy, yfy = np.meshgrid(x, yf, indexing="ij")
 
 rho = np.full((nx, ny), rho_(xx, yy)).T
 vx = np.full((nx, ny), vx_(xx, yy)).T
@@ -80,7 +90,7 @@ def P_(x, y):
 
 #############################################################################################################################################################################
 
-result_dir = '2Dwave/'
+result_dir = "2Dwave/"
 if os.path.exists(result_dir):
     shutil.rmtree(result_dir)
 
@@ -89,6 +99,18 @@ def P_(x, y):
 P0cc = p.PrimitiveVariables(nx, ny)
 P0cc.init(rho, vx, vy, vz, Bxf, Byf, Bz, P)
 
-p.PhareMHD(P0cc, result_dir, nghost, 
-           boundaryconditions, reconstruction, slopelimiter, riemannsolver, constainedtransport, timeintegrator,
-           Dx, Dy, FinalTime, dumpvariables = dumpvariables)
+p.PhareMHD(
+    P0cc,
+    result_dir,
+    nghost,
+    boundaryconditions,
+    reconstruction,
+    slopelimiter,
+    riemannsolver,
+    constainedtransport,
+    timeintegrator,
+    Dx,
+    Dy,
+    FinalTime,
+    dumpvariables=dumpvariables,
+)

pybind.cmake

@@ -0,0 +1,42 @@
+
+SET(PYBIND_MIN_VERSION "2.5.0")
+
+function(get_pybind)
+
+  # Pybind errors with clang, it is default in GCC
+  # https://github.com/pybind/pybind11/issues/1604
+  if ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang")
+    set (PHARE_FLAGS ${PHARE_FLAGS} -fsized-deallocation)
+  endif()
+
+  message("downloading subproject pybind11")
+  set(PYBIND11_SRCDIR ${CMAKE_CURRENT_SOURCE_DIR}/subprojects/pybind11)
+
+  if (NOT EXISTS ${PYBIND11_SRCDIR})
+  message("cloning your mother  ${PYBIND11_SRCDIR}")
+    execute_process(
+      COMMAND ${Git} clone https://github.com/pybind/pybind11 ${PYBIND11_SRCDIR} --depth 1 -b master
+    )
+  else()
+    if(devMode)
+      message("downloading latest pybind11 updates")
+      execute_process(COMMAND ${Git} pull origin master WORKING_DIRECTORY ${PYBIND11_SRCDIR})
+    endif(devMode)
+  endif()
+
+  message("now adding subdir")
+  add_subdirectory(${PYBIND11_SRCDIR})
+
+endfunction(get_pybind)
+
+if (forceGetPybind)
+  get_pybind()
+else()
+
+  find_package(pybind11 ${PYBIND_MIN_VERSION} CONFIG QUIET)
+
+  if (NOT pybind11_FOUND)
+    get_pybind()
+  endif()
+
+endif(forceGetPybind)

src/ConstainedTransport.cpp → src/ConstrainedTransport.cpp

@@ -1,4 +1,4 @@
-#include "ConstainedTransport.hpp"
+#include "ConstrainedTransport.hpp"
 
 static const PhysicalConstants& pc = PhysicalConstants::getInstance(); 
 

src/ModularityUtils.hpp

@@ -4,7 +4,7 @@
 #include "Enums.hpp"
 #include "SlopeLimiter.hpp"
 #include "RiemannSolver.hpp"
-#include "ConstainedTransport.hpp"
+#include "ConstrainedTransport.hpp"
 #include "TimeIntegrator.hpp"
 
 class Interface;
@@ -28,4 +28,4 @@ CTFunction getCT(CTMethod ct);
 typedef ConservativeVariables (*IntegratorFunction)(ConservativeVariables&, double, double, double, int, BoundaryConditions, Reconstruction, Slope, Riemann, CTMethod, OptionalPhysics);
 IntegratorFunction getIntegrator(Integrator intg);
 
-#endif
+#endif

src/TimeIntegrator.hpp

@@ -9,7 +9,7 @@
 #include "ModularityUtils.hpp"
 #include "ConservativeVariables.hpp"
 #include "GodunovFlux.hpp"
-#include "ConstainedTransport.hpp"
+#include "ConstrainedTransport.hpp"
 #include "AddGhostCells.hpp"
 #include "ComputeJ.hpp"
 
@@ -21,4 +21,4 @@ ConservativeVariables TVDRK2(ConservativeVariables& Un, double Dx, double Dy, do
 
 ConservativeVariables TVDRK3(ConservativeVariables& Un, double Dx, double Dy, double Dt, int nghost, BoundaryConditions bc, Reconstruction rec, Slope sl, Riemann rs, CTMethod ct, OptionalPhysics OptP);
 
-#endif // TIME_INTEGRATOR_HPP_
+#endif // TIME_INTEGRATOR_HPP_